[2015-02-21 07:55:39] Beginning TopHat run (v2.0.13)
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[2015-02-21 07:55:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-21 07:55:40] Checking for Bowtie index files (genome)..
[2015-02-21 07:55:40] Checking for reference FASTA file
[2015-02-21 07:55:40] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-21 07:55:53] Preparing reads
	 left reads: min. length=101, max. length=101, 23626409 kept reads (236716 discarded)
[2015-02-21 08:14:00] Mapping left_kept_reads to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 
[2015-02-21 08:58:52] Mapping left_kept_reads_seg1 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (1/4)
[2015-02-21 09:04:24] Mapping left_kept_reads_seg2 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (2/4)
[2015-02-21 09:09:37] Mapping left_kept_reads_seg3 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (3/4)
[2015-02-21 09:14:52] Mapping left_kept_reads_seg4 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (4/4)
[2015-02-21 09:22:03] Searching for junctions via segment mapping
[2015-02-21 09:28:27] Retrieving sequences for splices
[2015-02-21 09:29:04] Indexing splices
[2015-02-21 09:30:38] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2015-02-21 09:33:12] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2015-02-21 09:35:47] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2015-02-21 09:38:22] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-02-21 09:41:26] Joining segment hits
[2015-02-21 09:47:31] Reporting output tracks
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[2015-02-21 10:03:18] A summary of the alignment counts can be found in 6M/align_summary.txt
[2015-02-21 10:03:18] Run complete: 02:07:38 elapsed